similar to: Error when running Conditional Logit Model

Hi, I am playing with clogit(case~spontaneous+induced+strata(stratum),data=infert) from clogit help file. This line works. 1. But, why strata(stratum) doesn't have a coefficient like spontaneous and induced? 2. When I remove strata(stratum) from the command, this function seems to keep running forever. Why? 3. I think the equation for clogit looks like P=1/(1+

--begin inclusion -- I have a matched-case control dataset that I'm using conditional logistic regression (clogit in survival) to analyze. I'm trying to conduct k-folds cross validation on my top models but all of the packages I can find (CVbinary in DAAG, KVX) won't work with clogit models. Is there any easy way to do this in R? -end inclusion -- The clogit funciton is simply a

I have a case-control study that I'm analysing using the conditional logistic regression function clogit from the survival package. I would like to calculate the AICc of the models I fit using clogit. I have a variety of scripts that can calculate AICc for models with a logLik method, but clogit does not appear to use this method. Is there a way I can calculate AICc from clogit in R? Many

Dear R-help, I'm doing conditional logit regression for a discrete choice model. I want to know whether there's a way to get the fitted probabilities. In Stata, "predict" works for clogit, but it seems that in R "predict" does not. Thank you very much! Best wishes. Sincerely, Min -- Min Chen Graduate Student Department of Agricultural,

Hi, I have a script that takes a subset of genes on a microarray and tries to fit a coxph model to the expression values for each gene. This seems to work fine but in some cases it produces warnings and/or errors. For example: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In fitter(X, Y,

hi, I applied coxph to my matrix of 300 samples and 215 variables and got the following error Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, 26% of time data is censored and here

R list: I am using a 'for' loop to run a number of different models (stratified by different variables) with coxph. The data becomes sparse when some strata are used causing the model to become unstable. The following error occurs and the analysis is terminated. >Error in fitter(X, Y, strats, offset, init, control, weights = weights, : (converted from warning) Loglik

hello, I just installed R-3.4.0 from scratch: $ sudo apt install r-base but when I try > library(survival, lib.loc = "/usr/lib/R/library") > fit <- coxph(Surv(exit, event) ~ x, data = mort) I get Error in fitter(X, Y, strats, offset, init, control, weights = weights, : object 'Ccoxmart' not found I was told on R-help that I need to >

Hi, I want to fit multiple cox models using the coxph() function. To do this, I use a for-loop and save the relevant results in a separate matrix. In the example below, only two models are fitted (my actual matrix has many more columns), one gives a warning message, while the other does not. Right now, I see all the warning message(s) after the for-loop is completed but have no idea which model

Dear R-helpers: I am trying to fit a multivariate Cox proportional hazards model, modelling survival outcome as a function of treatment and receptor status. The data look like below: # structure of the data str(sample.data) List of 4 $ survobj : Surv [1:129, 1:2] 0.8925+ 1.8836+ 2.1191+ 5.3744+ 1.6099+ 5.2567 0.2081+ 0.2108+ 0.2683+ 0.4873+ ... ..- attr(*, "dimnames")=List of 2

Hi, I am getting errors of the following kind. I can't seem to point the source of the error. I would greatly appreciate any advice. Many thanks and good day, -Melinda Error message : ---------------- "Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights,..." Details : --------- E is a vector of survival times (or censored

Hi, I am running a simulation study with the survival::coxph. Some of the simulations result in problematic fits due to flat partial likelihood. So, you get the warning message: Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, ... : Loglik converged before variable 2 ; beta may be infinite. How can I keep track of the simulations which yield any kind of

Hi everyone, I encountered a problem using the coxph function for the conditional logistic regression. I am trying to do some simulations and I really don’t understand a mistake which happened maybe only 1 time among more than 1,000 simulations. What appeared on the screen is the following: Error in fitter(X,Y,strats,offset,init,control,weights=weights,: NA/NaN/Inf in a foreign function (arg

Am Dienstag, 25. April 2017, 08:50:34 schrieb Dirk Eddelbuettel: > On 25 April 2017 at 14:58, G?ran Brostr?m wrote: > | hello, > | > | I just installed R-3.4.0 from scratch: > | > | $ sudo apt install r-base > | > | but when I try > | > | > library(survival, lib.loc = "/usr/lib/R/library") > | > fit <- coxph(Surv(exit, event) ~ x, data =

Hi, I'm trying to use the R Survival analysis on a windows 7 system. The input data format is described at the end of this mail. 1/ I tried to perform a survival analysis including stratified variables using the following formula. cox.xtab_miR=coxph(Surv(time, status) ~ miR + strata(sex,nbligne, age), data=matrix) and obtain the following error message Warning message: In fitter(X, Y,

Hi, Just wondering, how do you capture "warning messege"s from R? I'm using Rpy (the python plug-in for R). I guess those are not python exception so I couldn't use the "try" block. For example: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, MPR Regards, Kylie-Anne Richards

Dear R users: I am not entirely convinced that clogit gives me the correct result when I use pspline() and maybe you could help correct me here. When I add a constant to my covariate I expect only the intercept to change, but not the coefficients. This is true (in clogit) when I assume a linear in the logit model, but the same does not happen when I use pspline(). If I did something similar

This is a simple R program that I have been trying to run. I keep running into the "singular matrix" error. I end up with no sensible results. Can anyone suggest any changes or a way around this? I am a total rookie when working with R. Thanks, Rasika > library(survival) Loading required package: splines > args(coxph) function (formula, data, weights, subset, na.action, init,

Hello, I have a couple of questions with regards to fitting a coxph model to a data set in R: I have a very large dataset and wanted to get the baseline hazard using the basehaz() function in the package : 'survival'. If I use all the covariates then the output from basehaz(fit), where fit is a model fit using coxph(), gives 507 unique values for the time and the corresponding cumulative

Hi all: My data has 3 variables: age(3levels : <30y=1 30-50y=2, >50y=3) gender(Male=0, Female=1) CD4 cell count(raw lab measurement) y(1:death 0:alive) I perform logistic regression to find out the factors that influence y. result<-glm(y ~ factor(age) + factor(gender) + CD4,family = binomial) >From the result,I can get OR(Odds Ratio) of gender via exp(Estimate of Female,